a b s t r a c tSeparation of milligram amounts of heparin oligosaccharides ranging in degree of polymerization from 4 to 32 is achieved within 6 h using continuous elution polyacrylamide gel electrophoresis (CE-PAGE) on commercially available equipment. The purity and structural integrity of CE-PAGE-separated oligosaccharides are confirmed by strong anion exchange high-pressure liquid chromatography, electrospray ionization Fourier transform mass spectrometry, and two-dimensional nuclear magnetic resonance spectroscopy. The described method is straightforward and time-efficient, affording size-homogeneous oligosaccharides that can be used in sequencing, protein binding, and other structure-function relationship studies.Ó 2010 Elsevier Inc. All rights reserved.Heparin is a linear sulfated glycosaminoglycan (GAG) 1 consisting of 1 ? 4-linked iduronic or glucuronic acid (IdoA or GlcA) and glucosamine (GlcN) disaccharide building blocks with an average of 2.7 sulfo groups per disaccharide repeat ( Fig. 1). Heparin mediates a number of biological pathways through its interactions with various regulatory proteins such as growth factors, chemokines, cytokines, and protease inhibitors [1,2]. Structure-function relationship studies involving heparin-protein interactions often require purified heparin oligosaccharides of various sizes and sulfation states obtained through enzymatic depolymerization of heparin polysaccharide. The ability to prepare high-purity oligosaccharides in sufficient amounts for the X-ray crystallography, protein-GAG binding studies, and domain sequencing is critical for the development of new drug targets and potential GAG-based therapeutics.Fractionation and purification of heparin oligosaccharides can be achieved in several ways using strong anion exchange (SAX) chromatography [3][4][5], ion pairing reverse phase high-pressure liquid chromatography (IP-RP HPLC) [6][7][8], size exclusion chromatography (SEC) [9], and micropreparative polyacrylamide gel electrophoresis (PAGE) [10][11][12] in combination or alone. Under low-pH conditions, SAX chromatography separates GAG-derived oligosaccharides according to the number of sulfo groups. Bound oligosaccharides are eluted with an increasing salt gradient and must be desalted for most downstream applications. During the IP-RP HPLC separation, an alkyl ammonium mobile phase modifier interacts with the negatively charged carboxy and sulfo groups in heparin through the positively charged ammonium moiety. The alkyl chain of the modifier interacts with the alkyl chains of the reverse phase support, imparting longer retention times to the more highly sulfated oligosaccharides, which are eluted with an increasing organic solvent gradient. SEC separates the oligosaccharides by size and may be used with a volatile buffer such as 30 to 50 mM ammonium formate [13]. Native discontinuous PAGE affords unmatched resolution for separation of GAG-derived oligosaccharides and provides an additional analytical dimension during the process of GAG characterization [11,12]. ...